Taris is correct. You will be able to use the VG30 transmission with no modifications, as well as the factory s12 motor mounts. There's truly no issue with fitment whatsoever, the only reason I had to do any physical modification to anything was because the supercharger made the engine too tall for the hood to hide. Without it, it'll fit under a stock hood.
Here's a link to the album where I keep all my s12 documentation, might make it easier to find things -> http://s99.photobucket.com/albums/l297/Eternally_Defiant/s12%20stuff/
as far as the swap goes its relatively simple, there are only a few things you actually need to do. Foremost you have to decide on new engine management, the stock s12 ECU will not run the VG33 properly [nor will a Z31 Turbo ECU] both will flood the motor with fuel. As for me, I bought an Infiniti M30 ECU and sent it to Jim Wolf Technologies to be rewritten specifically for the purpose of running the motor. It gave me Consult connectivity to monitor the engine, and works like a dream. It was a little pricey, and I had to literally build an entire engine/ecu harness but it was worth it in the end. That's really the biggest decision you need to make.
Everything else is pretty minor. If you decide to, you can run Z31 headers but on the driver's side, the second tube won't clear the steering linkage so you'll have to have it cut and rewelded. You'll also have to purchase a VG30e oil dip stick tube and drill out a plug on the right side of the motor to relocate it to the other side if you wanna do aftermarket headers.
You can use the stock s12 oil pan and oil catch tube, you just have to modify the catch tube and the sump in the stock pan so they fit up properly. When bolted up to the VG33, the catch tube bends at the wrong angle and is a little too far forward for the s12 sump, you just have to bend the tube back and shorten it, and cut the sump a little. No biggie.
All the mechanical shit is the easy part. You'll be able to use all stock VG33 accessories and whatnots as for as A/C and P/S and all that...your biggest headache will be wiring. If you went with what I used as engine management you'll have to rewire the entire s12 harness using a combination of the VG33/Infiniti M30/s12 wiring diagrams kindly provided by their respective FSMs. I might guess that using aftermarket type engine management might limit this somewhat (I might be wrong on this, the VG33 has some differences than the s12 electrically), but I wanted stock reliability.
Anyway...that's mostly what I can think of at the moment. I do suggest you have at least three things at all times:
-patience
-determination
-drinks
Good luck! I'll be glad to answer questions or offer advice along the way, If I can help I will.